Alternatives and similar repositories for MutationalPatterns:

Users that are interested in MutationalPatterns are comparing it to the libraries listed below

• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated last year
• crazyhottommy / scCustomize
  Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆16Updated 3 years ago
• ait5 / CNApp
  CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…
  ☆20Updated 5 years ago
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• ShixiangWang / Variants2Neoantigen
  A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
  ☆29Updated 5 years ago
• ChongJenniferZhang / CLCA_WGS
  ☆25Updated last year
• TheJacksonLaboratory / BRCA-LRseq-pipeline
  Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.
  ☆14Updated 2 years ago
• campbio / Manuscripts
  ☆14Updated 3 years ago
• caravagnalab / mobster
  Model-based subclonal deconvolution from bulk sequencing.
  ☆33Updated 3 months ago
• eudoraleer / scasa
  SCASA: Single cell transcript quantification tool
  ☆21Updated last year
• ManchesterBioinference / IntegratingATAC-RNA-HiC
  scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper
  ☆24Updated 2 years ago
• UMCUGenetics / primary-met-wgs-comparison
  Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.
  ☆15Updated last year
• icbi-lab / NeoFuse
  NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
  ☆19Updated 2 years ago
• quevedor2 / aneuploidy_score
  R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…
  ☆16Updated 4 years ago
• PoolLab / ReferenceEnhancer
  ☆20Updated last year
• sigven / oncoEnrichR
  Explore the cancer relevance of your gene list
  ☆51Updated last month
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆32Updated 3 years ago
• dakwok / SSNIP
  The Spatial Splicing-derived Neoantigen Identifier Pipeline (SSNIP) allows for the precise characterization of neoantigens derived from c…
  ☆17Updated 2 weeks ago
• ylab-hi / ScanNeo
  A pipeline for identifying indel derived neoantigens using RNA-Seq data
  ☆30Updated 2 years ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 2 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• shbrief / CNVWorkflow_Code
  CNV analysis workflow code for the manuscript
  ☆13Updated 4 years ago
• salzman-lab / SICILIAN
  ☆22Updated 10 months ago
• wenweixiong / MARVEL
  ☆49Updated 8 months ago
• PoisonAlien / somaticfreq
  knowledge-based genotyping of cancer hotspots from the tumor BAM files
  ☆21Updated 3 years ago
• marrlab / CAR_T_TargetIdentification
  Computational identification of targets for CAR-T cell therapy in AML
  ☆16Updated 2 years ago
• yizhak-lab-ccg / RNA_MUTECt_WMN
  ☆23Updated 2 years ago
• dzhakparov / GeneSelectR
  ☆19Updated 10 months ago
• Niinleslie / MesKit
  A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations
  ☆36Updated 3 years ago